Patient throughput has become one of the most common measures of hospital performance in terms of patient satisfaction and operational efficiency. Throughout the country hospital emergency departments, which generally supply almost 50% of the inpatient population, face increased pressure on improving patient flow. Similarly performance of ORs, the largest revenue grosser for the hospital significantly affects the patient satisfaction considerably. In addition to employing a DMAIC - Lean Six Sigma approach to resolve these problems, In simulation has been used as an excellent tool to implement the Analyze and Improve phases of the six-sigma methodology. We used simulation, integrated with six sigma, to model the functioning of the Emergency Departments and Operating Rooms at several hospitals to identify, evaluate and recommend potential measures to improve patient throughput. Resource and process based solution measures are recommended from the simulation results. The implementation of these measures has notably improved patient throughput and reduced length of stay.